PLUMED 2.10.1 - User Guide

Cluster: XLence (UNIMI Dipartimento di Scienze Farmacologiche e Biomolecolari) Date: September 30, 2026 Installation: /sw/plumed/2.10.1/ (one build for login and compute nodes)

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📦 Version Information

PLUMED: 2.10.1 (latest stable release, July 2026), all modules MPI: OpenMPI 4.1.6 PyTorch CVs: LibTorch 2.13.0 (C++, CPU) in /sw/libtorch/2.13.0-cpu Trajectory formats: all VMD molfile plugins (Amber NetCDF, DCD, XTC, TRR, PDB, ...) GSL: 2.7.1 FFTW: 3.3.10

It does not depend on any Python environment.

Available versions

Module	Notes
plumed/2.10.1	default: use this one, with amber/26 and gromacs/2025.0
plumed/2.9	the previous version

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🚀 Loading the Module

module load plumed           # plumed/2.10.1

# Verify
plumed info --version        # 2.10
echo $PLUMED_KERNEL          # /sw/plumed/2.10.1/lib/libplumedKernel.so

The module sets PLUMED_KERNEL, which programs that load PLUMED at run time use (Amber 26, and the plumed Python package).

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💻 Integration with MD Codes

AMBER 26

Integration: loaded at run time through PLUMED_KERNEL

module load amber plumed

Enable it in the &cntrl namelist of the MD input (there is no -plumed command-line option):

 &cntrl
  ...
  plumed=1, plumedfile='plumed.dat',
 /

pmemd.cuda -O -i md.in -p system.prmtop -c input.rst -o md.out -r md.rst -x md.nc

Works with pmemd.cuda, pmemd, pmemd.MPI and sander.

GROMACS 2025.0

Integration: patched with PLUMED 2.10.1, kernel loaded at run time through PLUMED_KERNEL

module load gromacs          # gromacs/2025.0, also loads plumed/2.10.1
gmx_mpi mdrun -v -deffnm md -plumed plumed.dat

Multiple walkers and replica exchange (-multidir, -replex) need the same nsteps in every simulation; with -replex, PLUMED can print but not bias. See GROMACS.

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📖 Example PLUMED Input Files

1. Distance Restraint

# plumed.dat - Monitor distance between atoms 1 and 10
d1: DISTANCE ATOMS=1,10

# Add harmonic restraint
RESTRAINT ARG=d1 AT=0.5 KAPPA=100.0

# Print every 100 steps
PRINT ARG=d1 FILE=COLVAR STRIDE=100

2. Metadynamics

# Define collective variable
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17

# Metadynamics
METAD ARG=phi,psi SIGMA=0.2,0.2 HEIGHT=1.2 PACE=500 FILE=HILLS

# Print
PRINT ARG=phi,psi FILE=COLVAR STRIDE=100

3. Umbrella Sampling

# Distance
d1: DISTANCE ATOMS=1,100

# Umbrella potential
RESTRAINT ARG=d1 AT=1.0 KAPPA=1000.0

# Print
PRINT ARG=d1 FILE=COLVAR STRIDE=10

4. Coordination Number

# Coordination number
c1: COORDINATION GROUPA=1-10 GROUPB=11-50 R_0=0.3 NN=6 MM=12

# Moving restraint
MOVINGRESTRAINT ARG=c1 STEP0=0 AT0=5.0 KAPPA0=100.0 STEP1=100000 AT1=10.0 KAPPA1=100.0

PRINT ARG=c1 FILE=COLVAR STRIDE=100

5. PyTorch Collective Variables

d1: DISTANCE ATOMS=1,10
d2: DISTANCE ATOMS=5,20

# A model exported with TorchScript (e.g. from mlcolvar), taking d1 and d2 as inputs
cv: PYTORCH_MODEL FILE=model.ptc ARG=d1,d2
PRINT ARG=cv.node-0 FILE=COLVAR STRIDE=100

PLUMED evaluates these models on the CPU.

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🔧 PLUMED Standalone Tools

Driver (Reprocess Trajectories)

module load plumed

# Amber NetCDF trajectory
plumed driver --plumed plumed.dat --mf_netcdf traj.nc

# GROMACS trajectory
plumed driver --plumed plumed.dat --mf_xtc traj.xtc --trajectory-stride 10

The --mf_ options are named after the VMD plugins, not after the file extensions. To list them all:

plumed driver --help | grep -o -- "--mf_[A-Za-z0-9_]*"

Sum Hills (Free Energy from Metadynamics)

plumed sum_hills --hills HILLS --outfile fes.dat

Python Interface

The installation has no Python bindings. Install them in your own environment, and point them at this kernel:

module load plumed
pip install plumed           # in your own conda/venv environment

python3 << 'EOF'
import plumed

# Uses the kernel in $PLUMED_KERNEL
p = plumed.Plumed()
p.cmd("setNatoms", 10)
p.cmd("init")
p.cmd("readInputLine", "d: DISTANCE ATOMS=1,10")
p.cmd("readInputLine", "PRINT ARG=d FILE=output.dat")
EOF

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📊 Analysis Examples

Extract Free Energy Surface

# From metadynamics HILLS file
plumed sum_hills --hills HILLS --outfile fes_phi_psi.dat

# For 1D:
plumed sum_hills --hills HILLS --outfile fes_phi.dat --idw phi

# Plot with gnuplot
gnuplot << 'EOF'
set pm3d
set palette defined (0 "blue", 1 "white", 2 "red")
splot "fes_phi_psi.dat" u 1:2:3 w pm3d
EOF

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🐛 Troubleshooting

Amber: "+++ ERROR: You are trying to use an invalid plumed object. +++"

• module load plumed was not run, so PLUMED_KERNEL is not set

"Unknown action in input"

• Check PLUMED version: plumed info --version
• Check available actions: plumed info --list-actions

"Atom index out of bounds"

• Verify atom indices in your system
• PLUMED uses 1-based indexing

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📚 Documentation

Local: - Build, validation and choices: /sw/plumed/2.10.1/README-xlence.md

Online: - PLUMED Manual: https://www.plumed.org/doc-v2.10/user-doc/html/ - Masterclass: https://www.plumed.org/masterclass - NEST (collective variables library): https://www.plumed-nest.org/

Mailing List: - https://groups.google.com/g/plumed-users

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📝 Citation

Tribello, G.A., Bonomi, M., Branduardi, D., Camilloni, C., Bussi, G. PLUMED 2: New feathers for an old bird Computer Physics Communications 185, 604 (2014)

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🔄 Integration Summary

MD Code	PLUMED	How to Use
AMBER 26	2.10.1, at run time	module load amber plumed, plumed=1 in &cntrl
GROMACS 2025.0	2.10.1, patched, at run time	module load gromacs, gmx_mpi mdrun -plumed plumed.dat

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For questions contact: Cluster administrators Installation: September 30, 2026 Installed by: Claude Code + Uliano Guerrini